The first line of defense against dust and other irritants is prior to the trachea, where large particles of dust and debris are trapped and exhaled. After that, everything else passes directly into the lower airway where the next line of defense is made up of tiny hair-like projections called cilia. The Cilia trap smaller particles and move them back up the airway, much like an escalator. The final defense barrier exists deep in the lungs; within the Alveoli where tiny cleaning cells called Macrophages perform a microscopic cleaning function, removing dust and bacteria. A horse in a dusty environment (the traditional stable being a good example) will therefore be more prone to infection than a horse in a cleaner environment. The equine lung evolved to deal with fresh air, therefore it is important to minimize pollutants (dust) in order to maintain healthy function.

The Respiratory systems begins with the nostrils, which, during intense exercise, can expand a lot. The nostrils have an outer ring made of cartilage that holds them open during inhalation. A small pocket inside them called the nasal diverticulum, filters debris with the help of hairs that line te inner nostril. The nasal cavity also has the nasolacrimal duct, which serves to drain tears from the eyes and out the nose.

The nose passages have to Conchae on either side. These help increase the surface area to which air is exposed. The sinuses within the skull are able to drain through the nasal passage. The nasal passage joins to the larynx by the pharynx. The pharynx is about 15cm long in an adult horse. This includes the naspharynx, which protects the entrance to the auditory tubes, the oropharynx, which contains the tonsilar tissue, and the laryngopharynx.

In parallel to the main nasal passages, the horse has a complex system of paranasal sinuses - air filled spaces within the head which communicate with the respiratory tract, and serve to reduce the weight of the head. These consist of:

• Frontal sinuses: Occupy the dorsal (top) part of the skull, between the eyes. There are two, one on each side, divided by a bony septum. These communicates with the inside of the conchae, forming the concho-frontal sinuses. Drainage into the nasal passages is via the caudal maxillary sinus.
• Maxillary sinuses: Within the maxilla, above the tooth roots. Each is divided into two components, the Rostral maxillary sinus in front and the Caudal maxillary sinus behind. They do not communicate. In addition, each of these is subdivided into a medial (inside) and lateral (outside) component, by an incomplete bone wall that carries the infraorbital canal containing nerves and blood vessels. The close proximity to the tooth roots mean that as the teeth erupt with age, the maxillary sinuses become larger.
• Sphenopalatine sinuses: Small pouches medial (inside) to the Caudal maxillary sinus.

A flap of tissue called the soft palate blocks off the pharynx from the mouth (oral cavity) of the horse, except when swallowing. This helps to prevent the horse from inhaling food, but does not allow use of the mouth to breathe. When in respiratory distress, a horse can only breathe through its nostrils. For this same reason, horses also cannot pant as a method of thermoregulation, such as dogs or people do. Horses also have a unique aspect to their respiratory system called the guttural pouch. This is thought to equalize air pressure on the tympanic membrane. This is located between the horse's mandibles (teeth) and it fills with air when the horse swallows or exhales.

The larynx lies between the pharynx and the trachea (windpipe). It is made up of 5 pieces of cartilage which serves to open the glottis (vocal folds). The larynx allows the horse to "speak", but prevents the aspiration of food and helps control the volume of air that the horse inhales. The trachea is a tube that takes air from the oral cavity and into the lungs. It is held permanently open. Blood is carried into the lungs via the pulmonary artery, where it is oxygenated at the alveoli and then returned to the heart by the pulmonary veins.

The horse expands its lungs with the help of the diaphragm, a muscular piece of tissue that contracts away from the thoracic cavity, decreasing the pressure and pulling air into the lungs. When they're fully expanded, the lungs can reach as far as the 16th rib of the horse.

Respiration rates vary widely between horses, but the average resting rate of a horse falls between 12 and 32 breaths per minute. Heat or humidity can raise the horse's respiration rate, especially if the horse is dark, or in the sun. It will change if the horse becomes excited or upset or nervous. This makes it useful in determining the health of the animal. At a gallop, the horse breathes in rhythm with every stride. As the horse's ab muscles pull the hind legs forward in the "suspension" phase of the gallop, the organs within the abdominal cavity are pushed backward, therefore bringing air into the lungs and causing the horse to inhale. As the neck is lowered during the extended phase of the gallop, the hind legs move backwards and the "guts" of the horse more forward, pushing into the diaphragm and forcing air out of the lungs.

The horse's smell receptors are located in the upper nasal cavity. Due to the length of the nasal cavity, there is a large area of receptors, and the horse therefore has a better ability to smell than a human.. The horse can also pick up pheromones and other scents when the horse gives the Flehmen response. This forces air through the slits in the nasal cavity and into the vomeronasal organ. Unlike many other animals, the horse's Jacobson's Organ doesn't open into the oral cavity.